[R] Help with hclust() and plot()

[michael watson (IAH-C)]

Hi Sean

I obviously wasn't cut out for this.

Just to try it out, I tried:

>plot(1:8, 1:8, mar=c(5,4,4,2))

(this is the default according to the help)

All I got was:

"there were twelve warnings"

>warnings()
1: parameter "mar" couldn't be set in high-level plot() function

BUT in the help, the example is given as:

<highlevel plot> (..., <tag> = <value>)

So, I know I must be doing something stupid, but I have no idea what....

Mick

-----Original Message-----
From: Sean Davis [mailto:sdavis2 at mail.nih.gov] 
Sent: 21 May 2004 12:30
To: michael watson (IAH-C); sundar.dorai-raj at pdf.com
Cc: r-help
Subject: Re: [R] Help with hclust() and plot()


See ?par.  It is a long help, but pay particular attention to
par(mar=c(...)).  It changes margins on plots.

Sean

On 5/21/04 7:12 AM, "michael watson (IAH-C)"
<michael.watson at bbsrc.ac.uk>
wrote:

> OK, I have it working now
> I just read in my data a little differently and now it works
> 
> HOWEVER, now my labels shoot off the end of the plot - so the labels 
> are truncated as they hit the edge of the window.  This happens for 
> both horizontal and vertical dendrograms
> 
> I guess this is an argument to plot that I need to set, but which one 
> ? :-(
> 
> Thanks
> 
> Mick
> 
> -----Original Message-----
> From: michael watson (IAH-C)
> Sent: 21 May 2004 11:53
> To: sundar.dorai-raj at pdf.com
> Cc: R-Help (E-mail)
> Subject: RE: [R] Help with hclust() and plot()
> 
> 
> Hi
> 
> Thanks again, but it *still* doesn't work!  I used the following
> commands:
> 
>> eucomplete <- hclust(d = dist(p[, 2:13], method = "euclidean"), 
>> method
> = "complete")
>> eucomplete$labels
> [1] "1"  "2"  "3"  "4"  "5"  "6"  "7"  "8"  "9"  "10" "11" "12" "13" 
> "14" "15" [16] "16" "17" "18" "19" "20" "21" "22" "23" "24"
>> eucomplete$labels <- p[,1]
>> eucomplete$labels
> [1] NB Hippo S2_824   ME7 Hippo S2_0    ME7 Hippo S2_949  ME7 Hippo
> S2_952
> [5] ME7 Hippo S2_823  NB Hippo S2_819D  ME7 Hippo S2_772D ME7 Hippo 
> S2_#003
> [9] NB Hippo S2_818D  NB Hippo S2_1     NB Hippo S2_#010  NB Hippo
> S2_775D
> [13] NB Hippo S2_774D  NB Hippo S2_#009  NB Hippo S2_950   NB Hippo
> S2_826
> [17] NB Hippo S2_#007  NB Hippo S2_951   ME7 Hippo S2_#004 ME7 Hippo
> S2_820D
> [21] ME7 Hippo S2_#005 ME7 Hippo S2_773D ME7 Hippo S2_#006 ME7 Hippo 
> S2_822D 24 Levels: ME7 Hippo S2_#003 ME7 Hippo S2_#004 ... NB Hippo 
> S2_951
>> plot(as.dendrogram(eucomplete))
> 
> I get a lovely formatted dendrogram but the labels are still numbers 
> 1-24! :-(
> 
> As can be seen, I have changed eucomplete$labels to be the text I 
> want, but the plot command still writes out numbers :-(
> 
>> plot(eucomplete)
> 
> Does work, and I get the right labels.  But I want a dendrogram!
> 
> Thanks in advance for your help
> 
> Mick
> 
> 
> 
> -----Original Message-----
> From: Sundar Dorai-Raj [mailto:sundar.dorai-raj at PDF.COM]
> Sent: 20 May 2004 19:04
> To: michael watson (IAH-C)
> Cc: R-Help (E-mail)
> Subject: Re: [R] Help with hclust() and plot()
> 
> 
> 
> 
> michael watson (IAH-C) wrote:
> 
>> Hi
>> 
>> Thanks for that!  BUT if I use as.dendrogram, I can't use my labels 
>> anymore!
>> 
>> 
>>> plot(hclust(...etc), labels=p[,1])
>> 
>> 
>> Works fine.  But:
>> 
>> 
>>> plot(as.dendrogram(hclust(...etc)), labels=p[,1])
>> 
>> 
>> Gives me errors:
>> 
>> Error in axis(side, at, labels, tick, line, pos, outer, font, vfont, 
>> lty,  : location and label lengths differ, 6 != 24
>> 
>> I have 24 labels.  I have no idea where it gets 6 from!
>> 
>> My 'dendrogram' has '2 branches and 24 members total'.
>> 
>> SOOO, how do I get my dendrogram horizontal, or vertical for that 
>> matter, with useful labels instead of 1,2,3,4,5,etc
>> 
>> Thanks in advance for your help!
>> 
>> Mick
>> 
> 
> Mick,
>  Change the labels in hclust first:
> 
> data(USArrests)
> hc <- hclust(dist(USArrests), "ave")
> hc$labels <- 1:50
> dend1 <- as.dendrogram(hc)
> plot(dend1, horiz = TRUE)
> 
> --sundar
> 
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